Proteins from Anaerobic Fungi and Uses Thereof

ABSTRACT

Provided herein are novel proteins and protein domains from newly discovered anaerobic fungal species. The anaerobic fungal species have unique enzymatic capabilities, including the ability to digest diverse lignocellulosic biomass feedstocks and to synthesize secondary metabolites. The scope of the invention encompasses novel engineered proteins comprising glycoside hydrolase enzymes, dockerin domains, carbohydrate binding domains, and polyketide synthase enzymes. The invention further encompasses artificial cellulosomes comprising novel proteins and domains of the invention. The scope of the invention further includes novel nucleic acid sequences coding for the engineered proteins of the invention, and methods of using such engineered organisms to degrade lignocellulosic biomass and to create polyketides.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation application of and claims the benefit of priority to U.S. patent application Ser. No. 16/898,421, entitled “Novel Proteins from Anaerobic Fungi and Uses Thereof,” filed Jun. 10, 2020 and issued as U.S. Pat. No. 11,021,524, issued Jun. 1, 2021, which is a continuation of U.S. patent application Ser. No. 15/782,016, entitled “Novel Proteins from Anaerobic Fungi and Uses Thereof,” filed Jun. 6, 2018 and issued as U.S. Pat. No. 10,717,628, issued Jul. 21, 2020, which is a 35 USC 371 national stage filing of International Patent Application Number PCT/US2016/065579, entitled “Novel Proteins from Anaerobic Fungi and Uses Thereof filed on Dec. 8, 2016, which claims priority to U.S. Provisional Application Ser. No. 62/265,397 entitled “Novel Polyketide Synthase Domains from Fungal Organisms,” filed Dec. 9, 2015 and U.S. Provisional Application Ser. No. 62/296,064 entitled “Production of Biofuels from Novel Fungal Strains and Enzymes Derived Therefrom,” filed Feb. 16, 2016, the contents of which applications are hereby incorporated by reference in their entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grant number W911NF-09-D-0001 awarded by the United States Army. The government has certain rights in the invention.

REFERENCE TO SEQUENCE LISTING, A TABLE, OR A COMPUTER PROGRAM LISTING COMPACT DISK APPENDIX

The instant application contains a Sequence Listing which has been filed electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Dec. 6, 2016, is named UCSB007PCT_SL.txt and is 21,694,502 bytes in size.

BACKGROUND OF THE INVENTION

Microbial communities have evolved immense enzymatic capabilities. In particular, anaerobic fungi perform metabolic feats which potentially could be adapted for great benefit. For example, the efficient conversion of biomass into fuels could provide humankind with an inexpensive, unlimited, and environmentally sustainable source of energy. However, current biomass conversion technologies are not economically scalable due to the recalcitrance of woody biomass. While humans have struggled to effectively capture energy from biomass, anaerobic fungi efficiently convert such material into many billions of joules of energy each day, in the digestive tracts of herbivores. These organisms have evolved efficient enzymatic machinery to break down cellulosic material in lignin rich plant material.

In addition to efficiently breaking down biomolecules, anaerobic fungi are able to synthesize complex natural products which are difficult or impossible to make using synthetic chemistry. Fungi have rich enzymatic abilities which create a diversity of biologically active molecules. Roughly 40% of drugs in use today were derived from fungi, for example, including antibiotics such as penicillin, chemotherapeutics such as vincristine or vinblastine, and cholesterol-lowering drugs such as statins. The prevalence of useful biomolecules produced by fungi is enabled by their unique enzymatic capabilities.

While the potential of fungi to improve bioproduction technologies is huge, large numbers of fungal species cannot contribute because they are not amenable to culture, isolation, and study. Anaerobic fungi in particular are very difficult to culture compared to model organisms such as aerobic bacteria or yeast. The anaerobic fungi have therefore been severely underrepresented in bioprospecting efforts due to the bottlenecks associated with their study.

Advantageously, the inventors of the present disclosure have developed methodologies for the culture of anaerobic fungi. This development has enable the isolation and characterization of organisms which were never previously studied. From this work, novel species of gut fungi have been isolated and their transcriptomes have been sequenced, revealing a multitude of new genes and proteins that can be used in energy production, in the synthesis of novel compounds, and in other applications.

SUMMARY OF THE INVENTION

The inventors of the present disclosure have identified four novel species of anaerobic fungi and have identified numerous useful protein domains and nucleic acid sequences coding therefor. These novel sequences provide the art with new enzymatic tools. In one aspect, the invention is directed to methods and compositions of matter utilized in the production of biofuels from lignocellulosic biomass utilizing the novel domains of the invention. In one aspect, the scope of the invention encompasses novel catalytic domains applied in the digestion of lignocellulosic biomass. In another aspect, the scope of the invention encompasses structural components which are incorporated into enzyme complexes, such as cellulosomes. Disclosed herein are novel engineered scaffoldins, glycoside hydrolase enzymes, dockerins, cohesins, and domains therefrom, as well as other catalytic proteins and protein domains involved in the breakdown of plant material. In another aspect, the scope of the invention encompasses methods of producing biofuels utilizing the novel organisms described herein in bioreactors or like processes.

In yet another aspect, the scope of the invention encompasses methods and compositions of matter which are utilized in the production of secondary compounds, such as polyketides. In one aspect, the compositions of the invention encompass engineered polyketide synthase complexes comprising one or more novel domains of the invention. In another aspect, the scope of the invention encompasses methods of using the domains of the invention in the production of secondary compounds.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 is a conceptual diagram of a cellulosome. The cellulosome complex comprises a scaffoldin (104), comprising a plurality of cohesins (105). Enzymatic moieties comprising catalytic domains (106) are attached to the scaffold by the docking of dockerins (107) to complementary cohesion molecules in dockerin-cohesin complexes (111). The docked proteins further include carbohydrate binding entities (108). The cellulosome is anchored in the cell membrane (103) of a host cell (101) by an anchoring moiety such as a transmembrane helix (102). The cellulosome can digest a complex polymer (109) such as cellulose into monomers (110).

DETAILED DESCRIPTION OF THE INVENTION

Four novel anaerobic gut fungi were isolated and cultured. The organisms include Piromyces finnis isolated from horse feces, Neocallimastix californiae, isolated from goat feces, Anaeromyces robustus, isolated from sheep feces, and Neocallimastix sp S4, isolated from sheep feces.

Utilizing novel culture methods, the organisms were isolated and pure cultures were attained, enabling the performance of sequencing efforts. Next-generation sequencing techniques were then utilized identify sequences expressed by the fungal cells. DNA analysis tools were then used to identify domains present in the expressed proteins. By their homology to known sequences, numerous types of useful domains were identified, including catalytic domains and structural domains.

The several domains identified are provided in the sequence listing submitted herewith. Table 1 lists domain names and a description for each domain name which identifies a gene or gene family associated with the sequence, as assigned by bioinformatic tools.

Each domain is represented as a novel polypeptide sequence having a domain description based on its similarity to known proteins from other organisms. Each domain is also provided as a nucleic acid sequence coding for the disclosed polypeptides. The listed protein sequences are provided in standard one-letter amino acid code, as known in the art. The listed nucleic acid sequences comprise fungal cDNA sequences. In the nucleic acids sequence listings, A is adenine; C is cytosine; G is guanine; T is thymine; and N is any of the four bases. The codon preferences of the anaerobic fungi are generally in line with those of model organisms, although fungal sequences tend to have a higher A-T content.

It will be noted that in some cases, multiple variants of a domain are listed, having been derived from the same transcript sequence. This is due to the use of multiple genetic identification tools, which in some cases use diverging models to recognize, define, and annotate protein domains. These models recognize a number of unique features, such as the N- or C-termini of catalytic domains, key catalytic residues, etc, each with their own start and stop sites, resulting in overlapping domain annotations for some transcripts.

The present disclosure provides the art with a large number of novel protein domains and corresponding nucleic acid sequences that may be applied in various contexts. Domains which are applicable to the various compositions and methods described herein can be readily selected from the sequence listing submitted based on the domain labels and descriptions provided in Table 1.

TABLE 1 Domain labels, descriptions, and SEQ ID NO.'s. Protein Nucleic Seq ID Acid Seq. Domain Label Domain Description No.'s ID No.'s (Trans)glycosidases Glycosidase  1-155 13663-13818 1- 1-Phosphatidylinositol 156-157 13819-13820 PHOSPHATIDYLINOSITOL phosophodiesterase PHOSPHODIESTERASE- RELATED PROTEIN 4-PPantetheinyl_Trfase_SF 4′-phosphopantetheinyl 158-165 13821-13827 transferase 4′-phosphopantetheinyl 4′-phosphopantetheinyl 166-173 13828-13835 transferase transferase 6-blade_b-propeller_TolB- six-bladed beta-propeller domain  174 13836 like found in TolB protein 6hp_glycosidase Glycosidase- six hairpin type 175-322 13837-13984 9-O-ACETYL-N- 9-O-acetyl-N-acetylneuraminic 323-333 13885-13995 ACETYLNEURAMINIC acid deacetylase ACID DEACETYLASE- RELATED AAC-RICH MRNA CLONE AAC-RICH MRNA CLONE  334 13996 AAC4 PROTEIN-RELATED AAC4 PROTEIN-RELATED AB_hydrolase Alpha-beta hydrolase fold 335-450 13997-14112 domain found in hydrolytic enzymes Abhydrolase_5 Alpha-beta hydrolase fold 451-464 14113-14126 domain 5 found in hydrolytic enzymes Ac_transferase_dom Acyl Transferase Domain 465-578 14127-14240 ACCESSORY GLAND Accessory Gland Protein domain 579-583 14241-14245 PROTEIN ACP76A- with similarity to that found in RELATED flies Acetyl-CoA synthetase-like Acetyl CoA Synthetase 584-603 14246-14265 ACID PHOSPHATASE Acid phosphatase 604-623 14266-14285 RELATED ACP DOMAIN Acyl Carrier Protein 624-668 14286-14330 ACP-like Acyl Carrier Protein 669-714 14331-14376 ACPS Acyl Carrier Protein Synthase, a 715-722 14377-14384 phosphopantetheinyl transferase Acyl_carrier_prot-like Acyl Carrier Protein 723-767 14385-14429 Acyl_transf_1 Acyl Transferase 768-798 14430-14460 ACYL-COA Acyl CoA Thioesterase I  799 14461 THIOESTERASE I ADH_N Catalytic domain of alcohol 800-807 14462-14469 dehydrogenase adh_short Domain from short chain 808-823 14470-14485 dehydrogenase family adh_short_C2 Domain from short chain 824-832 14486-14494 dehydrogenase C2 family ADH_ZINC Domain from alcohol 833-835 14495-14497 dehydrogenase, zinc type ADH_zinc_N Domain from alcohol 836-851 14498-14513 dehydrogenase, zinc type ALCOHOL Domain from alcohol 852-862 14514-14524 DEHYDROGENASE dehydrogenase RELATED Aldolase_TIM beta/alpha barrel domain found 863-870 14525-14532 in aldolases ALPHA-L-FUCOSIDASE 2 Alpha-L-fucosidase 871-874 14533-14536 alpha/beta-Hydrolases Alpha-beta hydrolase fold 875-972 14537-14634 domain found in hydrolytic enzymes Aminotran_1_2 Class I/Class II 973-982 14635-14644 Aminotransferase AMP_BINDING AMP binding domain 983-999 14645-14661 AMP-binding_C C terminal domain of AMP 1000-1001 14662-14663 binding enzyme Arabinanase/ Member of 1002-1058 14664-14720 levansucrase/invertase Arabinanase/levansucrase/ invertase superfamily ARF/SAR SUPERFAMILY Member of small GTPASE 1059-1060 14721-14722 PROTEIN-RELATED superfamily AT18611P-RELATED Carbohydrate binding domain 1061-1062 14723-14724 B_KETOACYL_SYNTHASE Beta-ketoacyl-ACP synthase 1063-1094 14725-14756 Barwin-like endoglucanases Endoglocanase 1095-1204 14757-14866 Beta_cellobiohydrolase 1,4-beta cellobiohydrolase 1205-1286 14867-14948 Beta-D-glucan exohydrolase, Beta-D-glucan exohydrolase, C- 1287-1297 14949-14959 C-terminal domain terminal domain BETA-GALACTOSIDASE Glycoside hydrolase Beta- 1298-1303 14960-14965 Galasctosidase beta- beta- 1304-1309 14966-14971 Galactosidase/glucuronidase Galactosidase/glucuronidase domain domain BETA/GAMMA Beta-Gamma Crystallin 1310-1316 14972-14978 CRYSTALLIN Structural Protein Bgal_small_N Beta-galactosidase small chain 1317-1322 14979-14984 BNR BNR repeat sequence 1323-1324 14985-14986 Carb_bind Carbohydrate Binding Domain 1325-1327 14987-14989 Carbohydrate-binding domain Carbohydrate Binding Domain 1328-1333 14990-14995 CarboxyPept_regulatory_dom Regulatory domain of 1334-1337 14996-14999 carboxypeptidase CBD_carb-bd_dom Carbohydrate Binding Domain 1338-1344 15000-15006 CBD_IV Cellulose binding domain, Type 1345-1370 15007-15032 IV CBM_1 Fungal cellulose binding domain 1371-1419 15033-15081 CBM_10 Dockerin and Carbohydrate 1420-3705 15082-17367 Binding Domain, Type 10 CBM_2 Carbohydrate Binding Domain, 3706-3709 17368-17371 Type 2 CBM_4_9 Carbohydrate Binding Domain 3710-3714 17372-17376 CBM_6 Carbohydrate Binding Domain, 3715-3736 17377-17398 family 6 CBM-like Carbohydrate Binding Domain 3737-3740 17399-17402 CBM1_1 Carbohydrate Binding Domain 3740-3758 17403-17420 CBM1_2 Carbohydrate Binding Domain 3759-3841 17421-17503 CBM6 Carbohydrate Binding Domain, 3842-3850 17504-17512 family 6 Cellulase Cellulase 3851-3962 17513-17624 CELLULASE (GLYCOSYL Cellulase- glycosyl hydrolase 3963-3972 17625-17634 HYDROLASE FAMILY 5) family 5 PROTEIN-RELATED Cellulose docking domain, Carbohydrate Binding Domain 3973-6217 17635-19879 docketing Cellulose-binding domain Carbohydrate Binding Domain 6218-6254 19880-19916 CHB_HEX_C Chitinase- Chitobiase, C 6255-6262 19917-19924 terminal domain CHIT_BIND_I_1 Chitin Binding Site, Type 1, may 6263-6265 19923-19927 bind N-acetylglucosamine CHIT_BIND_I_2 Chitin Binding Site, Type 1, may 6266-6270 19928-19932 bind N-acetylglucosamine CHITIN DEACETYLASE 1- allantoinase/chitin deacetylase 1  6271 19933 RELATED Chitin_bind_1 Chitin Binding Site, Type 1, may 6272-6275 19934-19937 bind N-acetylglucosamine Chitin-bd_1 Chitin Binding Site, Type 1, may 6276-6282 19938-19944 bind N-acetylglucosamine CHITINASE Chitinase 6283-6291 19945-19953 Chitinase insertion domain Chitinase insertion domain 6292-6300 19954-19962 CHITINASE_18 Chitinase, family 18 6301-6303 19963-19965 Chitinase_insertion Chitinase insertion domain 6304-6312 19966-19974 Chitobiase/Hex_dom_2-like domain 2 of bacterial chitobiases 6313-6314 19975-19976 and beta-hexosaminidases ChtBD1 Chitin Binding Site, Type 1, may 6315-6318 19977-19980 bind N-acetylglucosamine CINNAMYL ALCOHOL cinnamyl-alcohol dehydrogenase 6319-6322 19981-19984 DEHYDROGENASE 2- RELATED ClpP/crotonase Crotonase like domain 6323-6333 19985-19995 ClpP/crotonase-like_dom Crotonase like domain 6334-6344 19996-20006 CoA-dependent CoA-dependent acyltransferases 6345-6349 20007-20011 acyltransferases ConA-like_subgrp Concanavalin A-like 6350-6375 20012-20037 lectins/glucanases Concanavalin A-like Concanavalin A-like 6376-6433 20038-20095 lectins/glucanases lectins/glucanases Condensation Condensation domain 6434-6436 20096-20098 CotH spore coat protein, involved in 6437-6584 20099-20246 plant cell wall binding Cystine-knot_cytokine Cystine-knot_cytokine  6585 20247 CYTH-like phosphatases Phosphatase- acts on 6586-6587 20248-20249 triphosphorylated substrates CYTH-like_domain Phosphatase- acts on 6588-6589 20250-20251 triphosphorylated substrates Dockerin_dom Dockerin domain 6590-7679 20252-21341 Dockerin_dom_fun Dockerin domain 7680-8910 21342-22572 DPBB_1 Lytic transglycolase 8911-8919 22573-22581 DUF1729 Domain of unknown function- 8920-8930 22582-22592 Found in acyl transferase domains DUF303 Domain of unknown function 8931-8946 22593-22608 DUF303, acetylesterase DUF4353 Domain of unknown function 8947-8949 22609-22611 ECH Enoyl-CoA hydratase 8950-8959 22612-22621 EGGSHELL eggshell 8960-8963 22622-22625 Endo-1-4-beta- Endo-1-4-beta-glucanase,  8964 22626 glucanase_dom2 domain 2 ENDO-1,4-BETA- Endo-1-4-beta-glucanase 8965-8998 22627-22660 GLUCANASE ENDOGLUCANASE Endoglucanse 8999-9022 22661-22684 Endoglucanase_F_dom3 Endoglucanse F, domain 3 9023-9055 22685-22717 ENTEROBACTIN Entorbactin Synthase  9056 22718 SYNTHASE COMPONENT Component F F Esterase Esterase 9057-9080 22719-22742 Expansin_CBD C-terminal carbohydrate binding 9081-9106 22743-22768 domain of expansin EXPANSIN_EG45 N terminal domain of expansin 9107-9127 22769-22789 EXTRACELLULAR Extracellular matrix glycoprotein 9128-9129 22790-22791 MATRIX GLYCOPROTEIN related domain RELATED FabD/lysophospholipase-like FabD/lysophospholipase-like 9130-9240 22792-22902 domain- found in hydrolases FAMILY NOT NAMED Not associated with known 9240-9338 22903-23600 sequences FASYNTHASE Fatty Acid Synthase 9339-9468 23601-23130 FATTY ACID SYNTHASE Fatty Acid Synthase- subunit 9469-9479 23131-23141 SUBUNIT BETA beta fCBD Cellulose binding domain 9480-9605 23142-23267 fn3_3 domain II of 9606-9609 23268-23271 rhamnogalacturonan lyase Fn3_assoc domain II of  9610 23272 rhamnogalacturonan lyase Fn3-like domain II of 9611-9619 23273-23281 rhamnogalacturonan lyase Galactose mutarotase-like Galactose mutarotase-like 9620-9626 23282-23288 domain- binds carbohydrates Galactose-bd-like Galactose binding domain-like 9627-9668 23289-23330 fold Galactose-binding domain- Galactose binding domain-like 9669-9727 23331-23389 like fold GDHRDH short-chain 9728-9748 23390-23410 dehydrogenases/reductase family GH_fam_N_dom domain is found towards the N 9749-9753 23411-23415 terminus of some glycosyl hydrolase family members, including alpha-L-fucosidases GH04125P-RELATED Serine protease inhibitor related  9754 23416 GH97_C Glycosyl-hydrolase 97, C-  9755 23417 terminal oligomerisation domain GH97_N Glycosyl-hydrolase 97, N-  9756 23418 terminal domain GLHYDRLASE10 Glycoside hydrolase family 10 9757-9889 23419-23551 domain GLHYDRLASE11 Glycoside hydrolase family 11 9890-9998 23552-23660 GLHYDRLASE16 Glycoside hydrolase family 16 9999-10013 23661-23675 GLHYDRLASE2 Glycoside hydrolase family 2 10014-10028 23676-23690 GLHYDRLASE26 Glycoside hydrolase family 26 10029-10054 23691-23716 GLHYDRLASE3 Glycoside hydrolase, family 3, 10055-10094 23717-23756 N-terminal GLHYDRLASE48 Glycoside hydrolase family 48 10095-10308 23757-23970 GLHYDRLASE6 Glycoside hydrolase family 6 10309-10791 23971-24453 GLHYDRLASE8 Glycoside hydrolase family 8 10792-10818 24454-24480 GLUCOSE-METHANOL- Glucose-methanol-choline 10819-10820 24481-24482 CHOLINE (GMC) oxidoreductase OXIDOREDUCTASE GLUCOSYLCERAMIDASE Glucosylceramidase 10821-10823 24483-24485 Glyco_10 Glycoside hydrolase family 10 10824-10858 24486-24520 Glyco_18 Glycoside hydrolase family 18 10859-10865 24521-24527 Glyco_hyd_65N_2 N-terminus of the glycosyl 10866-10870 24528-24532 hydrolase 65 family catalytic domain Glyco_hydr_30_2 Glycoside hydrolase family 30 10871-10873 24533-24535 Glyco_hydro_10 Glycoside hydrolase family 10 10874-10913 24536-24575 Glyco_hydro_11 Glycoside hydrolase family 11 10914-10949 24576-24611 Glyco_hydro_11/12 Glycoside hydrolase family 10950-10986 24612-24684 11/12 Glyco_hydro_114 Glycosyl-hydrolase family, 10987-10989 24685-24651 number 114potential endo-alpha- 1,4-polygalactosaminidase Glyco_hydro_13_b Glycoside hydrolase family 13 10990-10991 24652-24653 Glyco_hydro_16 Glycoside hydrolase family 16 10992-11001 24654-24663 Glyco_hydrol_8 Glycoside hydrolase family 18 11002-11010 24664-24672 Glyco_hydro_2 Glycoside hydrolase family 2 11011-11013 24673-24675 Glyco_hydro_2_C Glycoside hydrolase family 2 11014-11016 24676-24678 Glyco_hydro_2_N Glycoside hydrolase family 2- N 11017-11019 24679-24681 terminal domain Glyco_hydro_2/20_Ig-like Glycoside hydrolase, family 11020-11025 24682-24687 2/20, immunoglobulin-like beta- sandwich domain Glyco_hydro_26 Glycoside hydrolase family 26 11026-11032 24688-24694 Glyco_hydro_3 Glycoside hydrolase family 3 11033-11041 24695-24703 Glyco_hydro_3_C Glycoside hydrolase family 3- C 11042-11059 24704-24721 terminal domain Glyco_hydro_3_N Glycoside hydrolase family 3 - N 11060-11068 24722-24730 terminal domain Glyco_hydro_39 Glycoside hydrolase family 39 11069-11081 24731-24743 Glyco_hydro_43 Glycoside hydrolase family 43 11082-11129 24744-24791 Glyco_hydro_45 Glycoside hydrolase family 45 11130-11153 24792-24815 Glyco_hydro_48 Glycoside hydrolase family 48 11154-11186 24816-24848 Glyco_hydro_53 Glycoside hydrolase family 53 11187-11189 24849-24851 Glyco_hydro_6 Glycoside hydrolase family 6 11190-11270 24852-24932 Glyco_hydro_8 Glycoside hydrolase family 8 11271-11276 24933-24938 Glyco_hydro_88 Glycoside hydrolase family 88 11277-11278 24939-24940 Glyco_hydro_9 Glycoside hydrolase family 9 11279-11312 24941-24974 Glyco_hydro_97 Glycoside hydrolase family 97 11313 24975 Glyco_hydro_beta-prop five-bladed beta-propellor 11314-11361 24976-25023 domain found in some glycosyl hydrolases Glyco_hydro_catalytic_dom catalytic TIM beta/alpha barrel 11362-11510 25024-25172 common to many different families of glycosyl hydrolases Glyco_hydro-type_carb- Carbohydrate binding domain 11511-11517 25173-25179 bd_sub from glycoside hydrolases Glycoside Glycoside hydrolase/deacetylase 11518-11521 25180-25183 hydrolase/deacetylase family GLYCOSYL HYDROLASE Glycoside hydrolase family 43 11522-11560 25184-25222 43 FAMILY MEMBER Glycosyl hydrolase domain catalytic TIM beta/alpha barrel 11561-11562 25223-25224 common to many different families of glycosyl hydrolases GLYCOSYL HYDROLASE- related to known glycosyl 11563-11564 25225-25226 RELATED hydrolase domains Glycosyl hydrolases family 6, Glycosyl hydrolases family 6, 11565-11648 25227-25310 cellulases cellulases GLYCOSYL Glycosyl transferase related 11649-11669 25311-25331 TRANSFERASE-RELATED domain GLYCOSYL_HYDROL_F10 Glycoside hydrolase family 10 11670-11688 25332-25350 GLYCOSYL_HYDROL_F11_1 Glycoside hydrolase family 11 11689-11719 25351-25381 GLYCOSYL_HYDROL_F11_2 Glycoside hydrolase family 11 11720-11721 25382-25383 GLYCOSYL_HYDROL_F3 Glycoside hydrolase family 3 11722 25384 GLYCOSYL_HYDROL_F45 Glycoside hydrolase family 45 11723-11742 25385-25404 GLYCOSYL_HYDROL_F5 Glycoside hydrolase family 5 11743-11765 25405-25427 GLYCOSYL_HYDROL_F6_2 Glycoside hydrolase family 6 11766-11816 25428-25478 GLYCOSYL_HYDROL_F9_2 Glycoside hydrolase family 9- 11817-11844 25479-25506 signature found in endglucanases and other glycoside hydrolases GroES-like Similarity to GroES (chaperonin 11845-11882 25507-25544 10), an oligomeric molecular chaperone HMG_CoA_synt_C Hydroxymethylglutaryl- 11883-11888 245545-25550 coenzyme A synthase C-terminal domain HMG_CoA_synt_N Hydroxymethylglutaryl- 11889-11891 25551-25553 coenzyme A synthase N- terminal domain HotDog_dom domain found in thioesterases 11892-11921 25554-25583 and thiol ester dehydratase- isomerases HxxPF_rpt HxxPF-repeat domain. 11922 25584 This family is found in non- ribosomal peptide synthetase proteins. ICP-like ICP-like domain 11923 25585 Inhibitor_I42 Protease inhibitor 11924 25586 Inosine monophosphate Inosine monophosphate 11925-11933 25587-25595 dehydrogenase (IMPDH) dehydrogenase Integrin alpha N-terminal Integrin alpha N-terminal 11934-11937 25596-25599 domain domain KAZAL_1 serine proteinase inhibitor 11938 25600 ketoacyl-synt Beta-ketoacyl synthase 11939-11983 25601-25645 Ketoacyl-synt_C Beta-ketoacyl synthase, C- 11984-12027 25646-25689 terminal domain KR Ketoreductase 12028-12043 25690-25705 L domain-like Leucine rich repeat domain 12044-12047 25706-25709 LamGL LamG-like jellyroll fold 12048-12050 25710-25712 Laminin_G_3 This domain belongs to the 12051-12053 25713-25715 Concanavalin A-like lectin/glucanases superfamily LEUCINE-RICH REPEAT Leucine-Rich Repeat Receptor- 12054-12057 25716-25719 RECEPTOR-LIKE Like Kinase1 PROTEIN KINASE Lipase_GDSL Domain from GDSL esterases 12058-12067 25720-25729 and lipases Lipase_GDSL_2 Domain from family of 12068-12070 25730-25732 presumed lipases and related enzymes LRR Leucine rich repeat 12071-12082 25733-25744 LRR_1 Leucine rich repeat 12083-12090 25745-25752 LRR_4 Leucine rich repeat 12091-12093 25753-25755 LRR_6 Leucine rich repeat 12094 25756 LRR_8 Leucine rich repeat 12095-12098 25757-25760 LRR_SD22 Leucine rich repeat 12099-12101 25761-25763 LRR_TYP Leucine rich repeat- typical 12102-12116 25764-25778 subtype LYSOPHOSPHOLIPASE- Lysophospholipase related 12117 25779 RELATED domain MALONYL COA-ACYL Malonyl-CoA:acyl carrier 12118-12128 25780-25790 CARRIER PROTEIN protein transacylase TRANSACYLASE MaoC_dehydrat_N N-terminal domain of MaoC 12129-12137 25791-25799 dehydratase MaoC_dehydratas C-terminal doamin of MaoC 12138-12152 257800-25814 dehydratase Metallo-dependent Metallo-dependent phosphatases 12153-12202 25815-25864 phosphatases Metallo-depent_PP-like Metallo-dependent phosphatases 12203-12245 25865-25907 Metallophos Metallo-dependent phosphatases 12246-12281 25908-25943 Mucin Mucins, high molecular weight 12282-12283 25944-25945 glycoconjugates NAD(P)-bd_dom NADP binding domain 12284-12334 25946-25996 NAD(P)-binding Rossmann- NAD(P)-binding Rossmann-fold 12335-12384 25997-26046 fold domains domains NODB catalytic domain found in 12385 26047 members of carbohydrate esterase family 4 Oligoxyloglucan reducing Oligoxyloglucan reducing end- 12386-12397 26048-26059 end-specific specific cellobiohydrolase cellobiohydrolase Pectin lyase-like Pectin-lyase like domain 12398-12408 26060-26070 Pectin_lyas_fold Pectin lyase fold domain 12409-12417 26071-26079 Peptidase_S8 Peptidase_S8 12418-12421 26080-26083 Peptidase_S8/S53_dom domain found in serine 12422-12427 26084-26089 peptidases PERIPLASMIC BETA- Periplasmic Beta-glucosidase 12428-12437 26090-26099 GLUCOSIDASE-RELATED related domain PERIPLASMIC BROAD- Periplasmic broad specificity 12438-12441 26100-26103 SPECIFICITY esterase/lipase/protease ESTERASE/LIPASE/ PROTEASE PEROXISOMAL Peroxisomal multifunctional 12442-12445 2614-26107 MULTIFUNCTIONAL enzyme type 2 ENZYME TYPE 2 PHL pollen allergen PHL pollen allergen 12446-12462 26108-26124 PHOSPHOPANTETHEINE Prosthetic group of acyl carrier 12463-12473 26125-26135 protein PI-PLC-X PI-PLC X domain 12474 26136-26137 12475 PIPLC_X_DOMAIN PI-PLC X domain 12476-12478 26138-26140 PKS_AT Acyl Transferase domain 12479-12509 26141-26171 PKS_ER Enoyl Reductase 12510-12525 26172-26178 PKS_KR Ketoreductase 12526-12545 26179-26198 PKS_KS Ketosynthase 12546-12579 26199-26241 PKS_PP phosphopantetheine-binding 12580-12607 26242-26269 domain Plant lectins/antimicrobial Plant lectins/antimicrobial 12608-12612 26270-26274 peptides peptides PLC-like phosphodiesterases PLC-like phosphodiesterases 12613-12618 26275-26280 PLC-like_Pdiesterase_TIM- domain consisting of a TIM 12619-12622 26281-26284 brl beta/alpha-barrel, found in several phospholipase C like phosphodiesterases PLCXc Phosphatidylinositol-specific 12623-12624 26285-26286 phospholipase C, X domain PLP-dependent transferases PLP-dependent transferases 12625-12634 26287-26296 POLYKETIDE SYNTHASE- Related to sequences found in 12635-12679 26297-26314 RELATED PKS domains Polysac_deacetylase Polysaccharide deacetylase 12680-12683 26314-26345 Polysacc_deac_1 domain found in polysaccharide 12684-12687 26346-26349 deacetylase PP-binding phosphopantetheine-binding 12688-12727 26350-26389 domain Probable ACP-binding Probable ACP-binding domain 12728-12740 26390-26402 domain of malonyl-CoA of malonyl-CoA ACP ACP transacylase transacylase PROKAR_LIPOPROTEIN Prokaryotic lipoprotein domain 12741-12761 26403-26423 PROPROTEIN Proprotein convertase 12762-12764 26424-26426 CONVERTASE subtilisin/kexin type 9 SUBTILISIN/KEXIN PROSTAGLANDIN Prostaglandin reductase 1 12765-12767 26427-26429 REDUCTASE 1 domain PROTEIN C41A3.1 Protein C41A3.1 12768-12770 26430-26432 PS-DH Polyketide synthase, dehydratase 12771-12785 26433-26447 domain PT Polyketide product template 12786-12787 26448-26449 domain PURPLE ACID purple acid phosphatase 23 12788-12797 26450-26459 PHOSPHATASE 23 Purple acid phosphatase, N- Purple acid phosphatase, N- 12898-12829 26460-26491 terminal domain terminal domain Purple_acid_Pase_N Purple acid phosphatase, N- 12830-12861 26492-26523 terminal domain PyrdxlP- Pyridoxal phosphate-dependent 12862-12871 26524-26533 dep_Trfase_major_sub1 transferase, major region, subdomain 1 PyrdxlP- Pyridoxal phosphate-dependent 12872-12879 26534-26541 dep_Trfase_major_sub2 transferase, major region, subdomain 2 Rhamnogal_lyase Rhamnogalacturonate lyase 12880-12883 26542-26545 RhgB_N Rhamnogalacturonase B, N- 12884-12885 26546-26547 terminal domain RICIN Ricin 12886-12950 26548-26612 Ricin B-like lectins Ricin B-like lectins 12951-13037 26613-26699 RICIN_B_LECTIN Ricin B-like lectins 13038-13108 26699-26770 RicinB_lectin_2 Ricin B-like lectins 13109-13186 26771-26848 SCP-like Spore coat protein like domain 13187-13189 26849-26851 SCP2 Spore coat protein 2 13190-13192 26852-26854 SCP2_sterol-bd_dom SCP2 sterol-binding domain 13193-13195 26855-26857 SDRFAMILY Short-chain 13196-13207 26858-26869 dehydrogenase/reductase SERINE PROTEASE Serine protease inhibitor 13208-13215 26870-26877 INHIBITOR, SERPIN SERINE/THREONINE Serine/threonine protein kinase 13216 26878-26878 PROTEIN KINASE SERPIN Serine protease inhibitor 13217-13242 26879-26904 Serpins Serine protease inhibitor 13243-13253 26905-26915 SGNH hydrolase SGNH hydrolase domain 13252-13294 26916-26956 SGNH_hydro- SGNHhydro-type esterase 13295-13307 26957-26969 type_esterase_dom domain Six-hairpin glycosidases six-hairpin glycoside domain 13308-13389 26970-27051 Starch-binding domain-like Starch-binding domain-like 13392-13393 27052-27055 SUBTILASE_ASP Serine proteases, subtilase 13394-13395 27056-27057 family, aspartic acid active site SUBTILASE_HIS Serine proteases, subtilase 13396-13397 27058-27059 family, histidine active site. SUBTILASE_SER Serine proteases, subtilase 13398-13399 27060-27061 family, serine active site. SUBTILISIN Protease domain 13400-13407 27062-27069 Subtilisin-like Subtilisin-like protease domain 13408-13416 27070-27078 Thioesterase Thioesterase 13417-13419 27079-27081 Thioesterase/thiol ester Thioesterase/thiol ester 13420-13449 27082-27111 dehydrase-isomerase dehydrase-isomerase Thiolase-like Thiolase-like domain 13450-13544 27112-27206 Thiolase-like_subgr Thiolase-like_subgr 13545-13637 27207-27299 Thioredoxin-like Thioredoxin-like 13638 27300 Thioredoxin-like_fold Thioredoxin-like fold domain 13639 27301 TIGR00556 phosphopantethiene--protein 13640-13647 27302-27309 transferase domain TIGR01733 amino acid adenylation domain 13648 27310 TIGR01833 hydroxymethylglutaryl-CoA 13649-13650 27311-27312 synthase TRANS-2-ENOYL-COA Enoyl- CoA reductase 13651-13654 27313-27316 REDUCTASE, MITOCHONDRIAL UNCHARACTERIZED Uncharacterized 13655-13656 27317-27318 VCBS VCBS repeat domain 13657 27319 ZINC FINGER FYVE Zinc finger FYVE domain- 13658-13659 27320-27321 DOMAIN CONTAINING containing protein PROTEIN ZINC FINGER- Zinc finger containing protein 13660-13662 27322-27324 CONTAINING PROTEIN

ENGINEERED PROTEINS. The domains disclosed herein may be utilized in the creation of “engineered proteins.” As used herein, a “protein of the invention,” or an “engineered protein” will refer to a non-naturally occurring protein, wherein such protein comprises one or more domains selected from SEQ. ID NO: 1-13662. A non-naturally occurring protein means the protein is not found in any wild-type species, having been engineered by molecular biological techniques known in the art. For example, the engineered protein may comprise heterologous elements, i.e. elements from different species. Alternatively, the engineered protein may comprise an anaerobic fungal protein lacking heterologous elements, but wherein the elements of the protein have been modified in some way such that they differ from those of the native protein, for example by rearrangement, duplication, or deletion of elements.

The domains disclosed herein will impart various properties to the engineered proteins in which they are incorporated. In some cases, the domain will comprise a structural element and will impart a structural property to the engineered protein. In another embodiment, the domain will comprise a binding domain and will impart a binding affinity for specific binding partners. In other embodiments, the domain will comprise a catalytic domain and will impart an enzymatic activity to the engineered protein.

The various domains of SEQ ID NO: 1-13662 encompass a wide variety of domains having diverse properties. One of skill in the art may readily select a domain of the invention for incorporation into an engineered protein based on the putative functions assigned to the domain. The putative functions of various domains of SEQ ID NO: 1-13662 are listed as “domain descriptions” in Table 1. Methods of using the engineered proteins of the invention will be readily ascertained by the skilled practitioner based upon the properties of the one or more domains of SEQ ID NO: 1-13662 and any additional properties imparted by accessory elements in the engineered proteins.

The proteins of the invention may include chemically synthesized polypeptides and recombinantly produced polypeptides comprising the domain sequences disclosed herein. The scope of the invention will be understood to extend to derivatives of the disclosed domain sequences. The term “derivative,” as used herein with reference to the polypeptides of the invention refers to various modifications, analogs, and products based on the polypeptide sequences disclosed herein, as described below.

Protein derivatives of the invention include substantial equivalents of the disclosed amino acid sequences, for example polypeptides having at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% amino acid sequence identity to a disclosed domain and/or which retain the biological activity of the unmodified sequences.

Protein derivatives of the invention further include polypeptides disclosed herein which have been modified by such techniques as ubiquitination, labeling (e.g., with radioactive or fluorescent moieties), covalent polymer attachment, etc. Derivative proteins of the invention include post-translational modifications of the polypeptide including, but not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation, etc.

Proteins derivatives of the invention further include polypeptides differing from the sequences disclosed herein by amino acid substitutions. For example, amino acid substitutions that largely preserve the secondary or tertiary structure of the original polypeptide may be selected on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic properties of specific residues. Determination of which amino acid substitutions may be made while maintaining enzymatic and other activities of interest is within ability of one of ordinary skill in the art of protein engineering. The invention also comprises substitutions with non-naturally occurring amino acids, amino acid analogs, etc.

Proteins derivatives of the invention further include mutations in the disclosed polynucleotide sequence intentionally introduced to enhance or modify characteristics of the polypeptide, such as to alter post-translational processing, binding affinities (e.g. introduction of specific epitopes for antibody binding), degradation/turnover rate, industrial processing compatibility (e.g. optimized expression, purification, etc.) or other properties.

The invention further comprises truncated versions of the protein domains disclosed herein, for example C-terminal, N-terminal, or internal deletions encompassing, for example, 1-20 amino acids. The invention further comprises isolated functional units from the disclosed domain sequences, for example isolated binding domains, catalytic domains, and other motifs having useful structures or functions which may be used in isolation from the remainder of the protein.

The invention further comprises any of the disclosed polypeptides sequences which have been augmented with additional amino acids. For example, the invention also includes fusion proteins and chimeric proteins in which a disclosed polypeptide sequences or sub-sequences thereof is combined with other peptides, proteins, or amino acid sequences. Exemplary fusion or chimeric proteins include the disclosed domain polypeptide sequences, or sub-sequences thereof, which have been combined with functional sequences from different proteins. Such proteins may further include secondary polypeptide sequences that impart desired properties such as enhanced secretion, or which enable purification (e.g. His-Tags), immobilization, and other desirable properties.

The invention further includes antibodies that specifically recognize one or more epitopes present on the disclosed polypeptides, as well as hybridomas producing such antibodies.

POLYNUCLEOTIDE CONSTRUCTS. The scope of the invention further encompasses any nucleic acid construct which codes for an engineered protein of the invention or codes for an engineered multiple enzyme complex of the invention. For example, the nucleic acid constructs of the invention may include any non-naturally occurring nucleic acid construct which comprises one or more nucleic sequences selected from SEQ ID NO: 13362-27324 or SEQ ID NO: 27328-27330, (corresponding to the proteins of SEQ ID NO: 1-13662 and SEQ ID NO: 27325-27327). However, it will be understood that, due to the redundancy of the genetic code and the diverging codon preferences in different species, that nucleic acid sequences coding for the proteins of SEQ ID NO: 1-13662 and SEQ ID NO: 27325-27327 are not limited to the fungal derived sequences disclosed in SEQ ID NO: 13663-27324 and SEQ ID NO: 27328-27330, and may comprise any nucleic acid construct comprising a sequence coding for the selected domain.

The polynucleotide sequences of the invention encompass DNA, RNA, DNA-RNA hybrids, peptide nucleic acid (PNA) or any other DNA-like or RNA-like material. For clarity, the polynucleotide sequences disclosed herein do not encompass genomic DNA sequences as present in their natural source (e.g. native organism). The polynucleotide sequences of the invention do not contain introns or untranslated 3-prime and 5-prime sequences. The polynucleotide sequences encompass translated sequences only.

The nucleic acid constructs of the invention encompass sequences which are the reverse or direct complement of any of the disclosed nucleic acid sequences (or their derivatives, as described below). Polynucleotide constructs of the invention may comprise single-stranded or double-stranded polynucleotides and may represent the sense or the antisense strand. The nucleic acid constructs of the present invention also include nucleic acid sequences that hybridize to the disclosed nucleotide sequences or their complements under stringent conditions. Polynucleotide constructs of the invention include sequences having high sequence similarity to the disclosed sequences (and their derivatives), for example, sequences having at least 80% homology, at least 85% homology, at least 90% homology, at least 95% homology, or at least 99% homology.

The polynucleotide constructs of the invention further encompass constructs comprising sequences which are derivatives of the disclosed domain polynucleotide sequences. As used herein, with reference to domain polynucleotide sequences, the term “derivative” refers to complementary sequences, degenerate sequences, truncated or augmented sequences, modified sequences, and other polynucleotides based upon the disclosed sequences. One form of polynucleotide derivative contemplated within the scope of the invention is a polynucleotide comprising nucleotide substitutions. For example, utilizing the redundancy in the genetic code, various substitutions may be made within a given polynucleotide sequence that result in a codon which codes for the identical amino acid as coded for in the original sequence, and which such change does not alter the composition of the polypeptide coded by a polynucleotide. Such “silent” substitutions may be selected by one of skill in the art. Likewise, nucleotide substitutions are contemplated which result in an amino acid substitution, wherein the amino acid is of similar polarity, charge, size, aromaticity, etc., such that the resulting polypeptide is of identical or substantially similar structure and function as a polypeptide resulting from an unmodified sequence. Further, the invention also comprises nucleotide substitutions which result in amino acid substitutions which create a polypeptide derivative, as described above.

It is also understood by one of skill in the art that various nucleotide analogs, modified nucleotides, and other compositions may be substituted for the nucleotides of the disclosed DNA sequences and their derivatives, for example modified or non-naturally occurring nucleotides such as 5-propynyl pyrimidines (i.e., 5-propynyl-dTTP and 5-propynyl-dTCP), 7-deaza purines (i.e., 7-deaza-dATP and 7-deaza-dGTP). Nucleotide analogs include base analogs and comprise modified forms of deoxyribonucleotides as well as ribonucleotides.

Additionally, substitutions in a disclosed polynucleotide sequence may be made which enable the translation of polypeptides from the polynucleotide sequence within a specific expression system. For example, as the polynucleotides of the invention are isolated from fungal species, it is contemplated that the disclosed sequences may be modified as necessary to enable or optimize expression of proteins in eukaryotic, yeast, insect, plant, mammalian, or in other expression systems such as cell-free and chemical systems. The selection of proper substitutions for proper expression within a given expression system is within the skill of one in the art of molecular biology.

Polynucleotide derivatives of the invention also comprise augmented or chimeric sequences, wherein a disclosed polynucleotide sequence has been modified to include additional nucleotides. For example, a disclosed polynucleotide sequence, or subsequences thereof, may be ligated with additional polypeptide sequences which enhance expression (for example, promoter sequences), or which alter the properties of the resulting polypeptide, such as sequences which enhance secretion, enable isolation (e.g. sequences which code for His-Tags or like moieties), enable immobilization, or other useful sequences as known in the art.

The scope of the invention additionally includes vectors, comprising the polynucleotide constructs of the invention integrated into vectors. Exemplary vectors include plasmids, phages, and viral constructs which promote efficient maintenance, amplification, and transcription of the polynucleotide sequences in an expression system. The nucleic acid constructs may comprise sequences integrated into the genome of an organism by transduction techniques known in the art.

ENGINEERED ORGANISMS. In one aspect, the scope of the invention encompasses organisms which have been genetically engineered to express one or more engineered protein of the invention, i.e. proteins comprising the protein domains selected from SEQ. ID NO: 1-13662. The engineered organisms of the invention further encompass organisms which express any of the ScaA full proteins of SEQ ID NO: 27325-27327, or portions thereof. Likewise, engineered organisms may comprise the nucleic acid constructs of the invention, for example, with the nucleic acid sequences being transiently expressed by the organism or being stably integrated into the genome of the organism. In one implementation of the invention, the engineered organism is an organism expressing one or more of nucleic acid sequences selected from SEQ ID NO: 13663-27324 or SEQ ID NO: 27328-27330.

Engineered organisms of the invention may comprise any species, for example, fungal species, yeast, bacteria, plants, and other organisms genetically modified to produce one or more engineered proteins of the invention. The engineered organisms of the invention may further comprise cell lines, such as insect cell cultures, CHO cells, and other cell culture systems used in the production of recombinant proteins.

Engineered Enzymes for Bioprocessing.

The various inventions described herein may be applied in numerous bioprocessing methods. The present description is largely directed to bioprocessing methods for the digestion of lignocellulosic biomass into fermentable monomers. However, it will be understood that the engineered proteins and organisms described herein may be applied in other bioprocessing methods, for example, for the synthesis of chemicals from feedstocks, including polymers, biofuels, and others.

In one aspect, the engineered proteins of the invention encompass proteins which participate in the breakdown of lignocellulosic biomass. In one embodiment, the engineered proteins of the invention comprise a glycoside hydrolase or other enzyme capable of digesting a component of lignocellulosic materials. For example, the engineered enzyme of the invention may comprise a cellulase, glycosidase, esterase, SGNH hydrolase, endoglucanase, cellobiohydrolase, Beta-D-glucan exohydrolase, beta-glucanase, phosphatidylinositol phosphodiesterase, pectin lyase, fucosidase, glycoside hydrolase, glycosyl hydrolase, hemicellulsase, xyanlase, galactosaminoglycan glycanohydrolase, amylase, chitinase, β-glucuronyl hydrolase, trehalase, glucoamylase, β-glucuronyl hydrolase, or acid phosphatase. In one embodiment, the engineered protein of the invention is a glycoside hydrolase comprising one or more domains selected from the group consisting of SEQ ID NO: 1-155; SEQ ID NO: 1095-1309; and SEQ ID NO: 3851-3972; and SEQ ID NO: 9755-11844. In one embodiment, the invention comprises an organism comprising a polynucleotide sequence which codes for a domain selected from the sequences of SEQ ID NO: 1-155; SEQ ID NO: 1095-1309; and SEQ ID NO: 3851-3972; and SEQ ID NO: 9755-11844.

The scope of the invention encompasses methods of using engineered proteins comprising lignocellulose degrading enzymes to facilitate the breakdown of lignocellulosic biomass. In one such method, an engineered protein comprising a lignocellulose-degrading enzyme is produced in an engineered organism. Exemplary engineered organisms include Saccharomyces cerevisiae, Zymomonas mobilis, Escherichia coli, and Clostridium thermocellum. Systems which utilize such organisms in biofuel production are known in the art. For example, the successful heterologous expression of functional saccharization enzymes from a fungal organism in yeast has been previously demonstrated, as described in O'Malley et al., Evaluating expression and catalytic activity of anaerobic fungal fibrolytic enzymes native topiromyces sp E2 in Saccharomyces cerevisiae. Environmental Progress and Sustainable Energy 31:37-46, 2012.

In one such method, the engineered protein is produced by and is subsequently extracted from the organism. Purification or modification steps may be applied to the extracted enzyme. The enzyme may then be used in any applicable lignocellulosic bioprocessing system by contacting it with an appropriate substrate under suitable conditions for enzymatic action to occur. In one embodiment, the extracted enzyme is used as a component of an enzymatic cocktail, for example, an enzymatic cocktail used in the saccharification of cellulosic materials.

In an alternative implementation, an engineered protein comprising a lignocellulose degrading enzyme of the invention is expressed in an engineered organism, and the engineered organism is cultured with an appropriate lignocellulosic substrate to promote breakdown of the substrate.

Methods of using proteins comprising a lignocellulose degrading enzyme of the invention may be performed in any bioprocessing method, for example, in ethanol production from biomass.

MULTIPLE ENZYME CATABOLIC COMPLEXES. In another embodiment, the invention encompasses engineered enzymatic complexes. An engineered enzyme complex is a complex comprising multiple enzymes bound to a carrier or scaffold and further comprising one or more substrate binding moieties. Such multiple enzyme complexes may be used to process a substrate with high efficiency due to the presence of multiple complementary enzymatic moieties being held in proximity to the substrate by the substrate binding moieties.

The engineered enzyme complexes of the invention are based on the bacterial cellulosome. In anaerobic microorganisms, cellulolytic enzymes are not secreted freely into the extracellular medium, as is generally the case for aerobic microbes, but instead these enzymes assemble into large (MDa) multi-protein cellulolytic complexes called cellulosomes. Cellulosomes comprise various components. A first component is a non-catalytic protein that is anchored to the cell membrane of the host cell expressing the cellulosome, typically a scaffoldin or its equivalent. The scaffoldin comprises multiple domains called cohesins, which are sites to which functional moieties will attach. The functional moieties may comprise enzymes which comprise one or more dockerin domains. The dockerin domain will selectively bind complementary cohesion domains on the scaffoldin protein with high affinity. The celluolytic complex will typically further comprise one or more carbohydrate binding moieties which bind lignocellulosic substrate. This binding keeps the substrate in proximity to the catalytic enzymes present on the cellulosome, facilitating degradation of the substrate. A conceptual depiction of a cellulosome is depicted in FIG. 1.

In one aspect, the scope of the invention encompasses what will be referred to as an engineered enzyme complex. The engineered enzyme complex comprises: a scaffold protein; one or more catalytic proteins; and one or more substrate-binding proteins. In one embodiment, the one or more catalytic proteins and one or more substrate-binding proteins are bound to the scaffold protein by cohesion-dockerin interactions with complementary dockerin and cohesion elements being present on the scaffold and on the bound moieties. An engineered enzyme complex of the invention is any enzyme complex wherein one or more component is an engineered protein of the invention. Alternatively, the engineered enzyme complex of the invention is one comprising a scaffoldin protein selected from SEQ ID NO: 27325-27327 (for example, being coded for by nucleic acid sequences SEQ ID NO: 27328-27330).

Tools and methodologies for the creation of multiple enzyme complexes and organisms expressing them are known in the art. Cellulosomes and like enzyme complexes have been successfully produced wherein the type and precise placement of enzymes is possible, for example as described in Fujita et al., Synergistic saccharification, and direct fermentation to ethanol, of amorphous cellulose by use of an engineered yeast strain codisplaying three types of cellulolytic enzyme. Appl Environ Microbiol. 2004 February; 70(2):1207-12. Additional methods of producing engineered cellulosomes are described in United States Patent Application Publication Number 20150167030, entitled “Recombinant cellulosome complex and uses thereof,” by Mazolli; United States Patent Application Publication Number 20130189745, entitled “Artificial cellulosome and the use of the same for enzymatic breakdown of resilient substrates,” by Schwarz; and U.S. Pat. No. 9,315,833, entitled “Yeast cells expressing an exogenous cellulosome and methods of using the same,” by McBride.

In one implementation of the invention, the engineered multiple enzyme complex is an artificial cellulosome designed for the efficient digestion of lignocellulosic biomass, wherein the one or more catalytic proteins comprise a plurality of proteins which degrade lignocellulosic material, e.g. glycoside hydrolase proteins, and the one or more substrate-binding proteins comprise carbohydrate binding domains.

In one embodiment, the scaffold protein of the engineered enzyme complex is a scaffoldin protein comprising multiple cohesion domains. For example, the scaffoldin protein may comprise a scaffoldin protein selected from the group consisting of SEQ ID NO: 27325-27327. In another embodiment, the artificial cellulosome comprises a dockerin domain. In one embodiment, the dockerin domain comprises a dockerin domain selected from the group consisting of: SEQ ID NO: 1420-3705 and SEQ ID NO: 6590-8910. In another embodiment, the artificial cellulosome comprises one or more carbohydrate binding domains. For example, the carbohydrate binding domain may comprise a carbohydrate binding domain selected from the sequences of: SEQ ID NO: 1061-1062; SEQ ID NO: 1325-1333; SEQ ID NO: 1378-1419; SEQ ID NO: 3706-3850; SEQ ID NO: 3973-6254; and SEQ ID NO: 9480-9605. In one embodiment, the artificial cellulosome of the invention comprises one or more glycoside hydrolase proteins comprising one or more domains selected from the sequences of SEQ ID NO: 1-155; SEQ ID NO: 1095-1309; and SEQ ID NO: 3851-3972; and SEQ ID NO: 9755-11844.

The scope of the invention further extends to nucleic acid sequences which code for the various elements of the artificial cellulosomes. The scope of the invention further encompasses engineered organisms which express the various elements of the artificial cellulosome. The scope of the invention further encompasses methods of using such engineered organisms in the digestion of lignocellulosic biomass. It will be understood that the artificial cellulosomes of the invention comprise or are expressed in combination with anchoring moieties, secretory signals and other elements required for the expression, secretion, and assembly of cellulosomes, as known in the art.

The artificial cellulosomes of the invention enable components from two or more species to be advantageously combined. Enzymes from non-fungal species can be utilized in anaerobic fungal cellulosomes, or enzymes from anaerobic fungi can be used in non-fungal cellulosomes. For example, in one implementation, the novel dockerin domains of the invention derived from anaerobic fungi may be fused with enzymes or carbohydrate-binding moieties from other species, such as from yeast or aerobic bacteria, and these combined elements can be bound to scaffoldins from anaerobic fungi. In another implementation, dockerins from other species could be fused to catalytic proteins or carbohydrate binding domains from anaerobic fungi, facilitating the inclusion of these anaerobic fungal proteins in synthetic cellulosomes of other species. This exchange of enzymatic elements from divergent species aids in the creation of novel artificial cellulosomes having extended enzymatic capabilities beyond those of wild type enzymatic complexes. Such hybrid systems can, with a single organism, recapitulate digestive processes in the complex environment of the rumen, where fungal, yeast, and bacterial strains work in concert to digest complex biomass.

It will be understood that the engineered enzyme complexes of the invention are not limited to multiple enzyme complexes which degrade lignocellulosic material, and may be designed for efficient enzymatic action of any kind on any substrate, as determined by the selection of suitable catalytic enzymes and substrate-binding moieties.

Polyketide Synthases

A very large number of important drugs and biologically active compounds are from the group called polyketides. Polyketides are structurally diverse compounds created by multi-domain enzymes or enzyme complexes called polyketide synthases (PKSs). PKSs proteins are composed of various peptide domains, each of which has a defined function. Various classes of PKSs are known, including Type I, Type II, and Type III PKSs. The Type I PKSs may be classified as either iterative or modular.

The iterative PKSs comprise a single module. The creation of a polyketide is initiated by binding a starting material to the acyl-transferase (AT) domain, the starting material typically being Acetyl-CoA or malonyl-CoA. The bound starting material is then shuttled to the KS domain by an acyl carrier protein (ACP). An extender material, typically malonyl-CoA is then loaded into the complex by the AT domain and is added to the starter material by a condensation reaction catalyzed by the ketosynthase (KS domain). Additional domains may introduce modifications to the bound chain by catalytic action. Additional extension reactions and modification reactions occur until the polyketide chain has reached its final length, which is specific for each type of iterative PKS. The mechanisms by which final length is controlled are not known. When the polyketide has reached its final length, a thioesterase (TE) domain releases the completed polyketide. Thus, such PKSs are called “iterative” because the final product polyketide is produced in an iterative fashion by the repeated action of the domains to lengthen and modify the growing polyketide chain. The various enzymatic domains of the iterative PKSs are not always used in each cycle, allowing for more variability in final product composition.

In contrast, modular PKSs have multiple repeating modules, arranged from the N-terminal end of the PKS towards the C-terminal end. In each module, the AT, ACP, and KS domains are repeated, and each module also contains its own combination of catalytic domains. Chain elongation is initiated at the N-terminal end in the first module, and the growing chain is passed from module to module towards the C-terminal end, undergoing a single elongation and one or more enzymatic modifications at each step. At the C-terminal module, a thioesterase (TE) domain releases the completed polyketide.

Just as PKS domains can interact with one another, PKSs can interact, or form hybrid complexes, with non-ribosomal peptide synthases to form active compounds (e.g. the anticancer compound epothilone).

Various classes of enzymatic PKS domain are known, including:

-   -   keto reductase (KR) domains, which reduces ketone groups to         hydroxyl groups;     -   dehydratase domains (DH), which reduces hydroxyl groups to enoyl         groups;     -   enoyl reductase (ER) domains, which reduce enoyl groups to alkyl         groups;     -   methyltransferase (MT) domains, which transfer methyl groups to         the growing polyketide;     -   sulfohydrase domains (SH); and     -   product template domains, which determine the folding pattern of         the polyketide backbone.         Additional non-PKS catalytic domains that work in tandem with         PKS domains include aminotransferases, pyridoxal-phosphate         transferases and HMG-CoA synthases.

The specificity of substrates and products for the domains varies, as well as their order within PKSs. Accordingly, the different combinations the order of enzymatic domains within the PKS modules, and the different arrangements of modules within modular PKSs means that these enzymes can be configured to produce an immense range of final products.

The released polyketide may then be further modified by the action of additional enzymes, for example the addition of carbohydrate moieties or methyl groups. The further complexity of PKS systems enables even greater diversity of products, for example, two iterative PKSs can interact to form a common product (for example as in the synthesis of zearalenone). A PKS may also be fused with another enzyme to form a single enzyme (for example as known in the synthesis of fusarin C).

Accordingly, PKSs, due to their modular nature, including multiple domains arranged within a module, and multiple modules within an enzyme, present a potential platform for the synthesis of myriad biological products.

Engineered PKS's. Engineered PKS systems are known in the art and have been successfully utilized to create various novel end products, some of which have never been observed in nature. Various strategies exist for utilizing novel PKS enzymes, PKS modules, or PKS domains in the creation of diverse, potentially bioactive molecules. Exemplary PKS engineering techniques are described in U.S. Pat. No. 9,334,514, entitled “Hybrid polyketide synthases,” by Fortman et al.; U.S. Pat. No. 8,709,781, entitled “System and method for the heterologous expression of polyketide synthase gene clusters,” by Boddy et al.; and United States Patent Application Publication Number 20130067619, entitled “Genes and proteins for aromatic polyketide synthesis,” by Page and Gagne.

The current state of PKS engineering allows for the recombination and swapping of various PKS enzymes, modules, and domains, enabling novel means of synthesizing compounds using engineered enzyme systems. Accordingly, there is a need in the art for PKS enzymes, modules, and domains with novel functions, which such elements may be employed in engineered PKS systems. The novel PKS gene and protein sequences provide the art with novel tools for the creation of engineered PKS synthesis systems and enable the creation of novel compounds.

In one aspect, the scope of the invention encompasses engineered proteins comprising engineered PKS enzymes. The engineered PKS enzyme of the invention may comprise a modular PKS or an iterative PKS. In one embodiment, the engineered PKS enzyme of the invention comprises an acyl transerase domain. For example the engineered PKS may comprise an an acyl transferase domain selected from the sequences of SEQ ID NO: 465-578; SEQ ID NO: 768-798; and SEQ ID NO: 12479-12509. In one embodiment, the engineered PKS comprises an acyl carrier protein domain. For example, the acyl carrier protein domain may comprise an acyl carrier domain selected from the sequences of SEQ ID NO: 604-767 and SEQ ID NO: 12463-12473. In one embodiment, the engineered PKS comprises a ketosynthase domain. For example, the ketosynthase domain may comprise a ketosynthase domain selected from the sequences of SEQ ID NO: 12546-12579. In one embodiment, the engineered PKS comprises a thioesterase domain. For example, the thioesterase domain may comprise a thioesterase domain selected from the sequences of SEQ ID NO: 13417-13449. In one embodiment, the engineered PKS comprises a ketoreductase domain. For example, the ketoredudctase domain may comprise a ketoreductase domain selected from the sequences of SEQ ID NO: 12028-12043 and SEQ ID NO: 12526-12545. In one embodiment, the engineered PKS comprises a dehydratase domain. For example, the dehydratase domain may comprise a dehydratase domain selected from the sequences of SEQ ID NO: 12129-12152 and SEQ ID NO: 12771-12785. In one embodiment, the engineered PKS comprises an enoyl reductase domain. For example, the enoly reductase domain may comprise an enoyle reductase domain selected from the sequences of SEQ ID NO: 12510-12525 and SEQ ID NO: 13651-13654. In one embodiment, the engineered PKS of the invention comprises a product template domain. For example, the product template domain may comprise a product template domain selected from the sequences of SEQ ID NO: 12786-12787. The scope of the invention further encompasses engineered proteins which are not PKS enzymes, but which contain any of the aforementioned PKS domains.

The scope of the invention further includes engineered accessory enzymes, which, as used herein, are engineered proteins with functions accessory to PKS enzymes. In one embodiment, the engineered protein comprises an aminotransferase domain selected from SEQ. ID NO: 973-982. In one embodiment, the engineered protein comprises a pyridoxal-phosphate transferase domain selected from SEQ. ID NO 12862-12879. In one embodiment, the engineered protein comprises a HMG-CoA synthase domain selected from SEQ. ID NO 11883-11891.

The scope of the invention further encompasses nucleic acid constructs which code for any of the aforementioned engineered PKS enzymes or engineered accessory enzymes. Furthermore, the scope of the invention encompasses engineered organisms which express any of the aforementioned engineered PKS enzymes or which comprise a nucleic acid construct coding therefor. Exemplary engineered PKS organisms include fungal species, bacterial species, yeast species, or plant species. The scope of the invention further encompasses methods of creating complex molecules, including polyketides, utilizing the engineered PKS enzymes and/or organism expressing such engineered PKS enzymes, wherein suitable substrates are exposed to such engineered PKS enzymes and/or organism expressing such engineered PKS enzymes under conditions which facilitate the synthesis of desired end-products.

Biofuel Production Using Novel Anaerobic Fungal Strains

Lignocellulosic material, or biomass, is a renewable and abundant material and represents a potential feedstock for energy and chemical production. However, the sugars contained in lignocellulosic materials are locked in a complex of lignin, hemicellulose and cellulose and other plant cell wall components. Currently, to extract fermentable sugars from these recalcitrant feedstocks, lignin and hemicellulose must be separated from the biomass prior to converting cellulose into monosaccharides. As a result, bioprocessing of crude biomass entails energy-intensive pretreatment steps, and the addition of an expensive and often inefficient cocktails of cellulolytic enzymes.

In contrast, anaerobic gut fungi that are resident in the gut of herbivores routinely and efficiently degrade cellulose in complex, lignin-rich biomass. This is achieved through both mechanical and enzymatic processes: colonizing fungi develop a highly branched rhizoidal network, or rhizomycelium, that penetrates and exposes the substrate to attack by secreted cellulases. Importantly, this unique invasive strategy for plant cell wall degradation enables gut fungi to colonize and decompose complex cellulosic feedstocks. Anaerobic gut fungi degrade plant particulates of dissimilar sizes at nearly the same rate, whereas the degradation rates of eubacterial populations steadily decrease with increasing particle size. Therefore, anaerobic gut fungi may serve as a means to degrade diverse biomass feedstocks to useful bioenergy compounds, without the need for expensive pretreatment, greatly reducing the cost and increasing the efficiency of biomass conversion to useful products.

Accordingly, there is a need in the art for novel organisms capable of efficient conversion of biomass to usable fuel materials, and for methods of culturing such organisms. The four previously undescribed species of anaerobic fungal gut organisms described herein fulfill this need in the art, being capable of breaking down plant material to produce ethanol, hydrogen, and other useful materials. Grown under anaerobic culture conditions, each of the four organisms is capable of degrading a wide range of lignocellulosic materials. For example, the organisms can metabolize reed canary grass, glucose, fructose, avicel, and filter paper, demonstrating an ability to break down a wide range of biomass materials.

In addition to cellulosomes, which convert plant material into fermentable sugars, anaerobic fungi possess hydrogenosomes that convert the released sugars to hydrogen gas following glycolysis. Hydrogenosomes are intracellular membrane-bound organelles that are analogous to the mitochondria of aerobic microbes. In general, they metabolize malate and pyruvate to H₂, CO₂, formate, and acetate, generating energy in the form of ATP. The four novel organisms described herein are each capable of hydrogen production from a range of feedstocks.

Accordingly, in one aspect, the invention comprises the use of Piromyces finnis, Neocallimastix californiae, Anaeromyces robustus, and/or Neocallimastix sp S4 in the conversion of biomass feedstocks into ethanol, hydrogen, and other useful materials. The basic process of the invention comprises introducing biomass feedstocks into a bioreactor vessel wherein culture conditions amenable to organism growth and metabolism are maintained, allowing colonization and digestion of biomass by the organisms, and ongoing or subsequent harvesting of end-products.

Anaerobic bioreactors and fungal bioreactors are known in the art. For example, exemplary fungal and/or anaerobic bioreactors are described in: Moreira et al., Fungal Bioreactors: Applications to White-Rot Fungi, Reviews in Environmental Science and Biotechnology, 2003, Volume 2, Issue 2-4, pp 247-259; Martin, An Optimization Study of a Fungal Bioreactor System for the Treatment of Kraft Mill Effluents and Its Application for the Treatment of TNT-containing Wastewater, in Bioreactors, Auburn University Press, 2000; Palma et al., Use of a fungal bioreactor as a pretreatment or post-treatment step for continuous decolorisation of dyes, 1999, WATER SCIENCE AND TECHNOLOGY; 40, 8; 131-136; US Patent Publication Number US 20100159539 A1, Methods and systems for producing biofuels and bioenergy products from xenobiotic compounds, by Ascon; China Patent Publication 101374773, Method and bioreactor for producing synfuel from carbonaceous material, by Khor; and US Patent Publication Number 20100196994 A1, Fungi cultivation on alcohol fermentation stillage for useful products and energy savings, by van Leeuwen. Bioreactor designs amenable to the growth of the gut fungi described herein may be readily developed utilizing knowledge of the growth conditions optimal for anaerobic gut fungi growth and activity. The invention encompasses the use of any type of bioreactor design, including batch reactors, flow-through reactors, and other bioreactor designs known in the art.

Anaerobic fungi are may be grown under substantially anaerobic conditions. Optimal temperatures for the growth and biomass digestive activity of such organisms is in the range of 25-40 C, preferably in the range of 30-40 C. Cultures may be grown grown without agitation, on soluble or insoluble carbon sources, under a head space of 100% CO₂ gas. Liquid culture medium is preferred for growth and maintenance of the anaerobic fungi.

The culture media used to grow anaerobic fungi may be any known in the art, for example formulations based on those used for the cultivation of rumen bacteria. For the most part, they are complex, non-defined media (pH 6.5-6.8) and contain up to 15% (v/v) clarified rumen fluid, but chemically defined media can be used as well, as described in Marvin-Sikkema, F. D., Lahpor, G. A., Kraak, M. N., Gottschal, J. C., Prins, R. A., Characterization of an anaerobic fungus from llama faeces. J. Gen. Microbiol. 1992, 138, 2235-2241. Although phosphate buffers may be used, a preferred buffer is bicarbonate with CO₂ in the head space contributing to the buffering system. Chemical reducing agents (e.g., sodium sulfide and/or L-cysteine hydrochloride) are added to culture media pre- or post-autoclaving, after the majority of the O₂ has been removed from culture solutions by boiling and gassing with CO₂. These procedures ensure that low oxygen levels of the culture medium are maintained such that anaerobic fungal growth can be supported.

The methods of the invention encompass various steps. In a first step, biomass is fed into the bioreactor. Any form of cellulosic or lignocellulosic material may be utilized in the bioreactors and methods of the invention. Biomass includes, but is not limited to, herbaceous material, agricultural residues, forestry residues, municipal solid wastes, waste paper, and pulp and paper mill residues. Exemplary feedstocks include corn stover, canary reed grass, swtichgrass, Miscanthus, hemp, poplar, willow, sorgum, sugarcane, bamboo, eucalyptus. Additional feedstocks include byproducts of industrial processes, such as pulping liquor (a byproduct of paper production).

Generally, it is preferred that the biomass feedstocks utilized in the processes of the invention be pre-processed to some degree prior to digestion by the fungal organisms. Preprocessing steps include grinding or other mechanical treatments which break the biomass into small particulates that may be more easily colonized and digested by the fungal organisms. Particulates in the range of 0.1 to 10 mm diameter, for example, may be used.

The biomass material is then inoculated with one or more fungal strains selected from the group consisting of Piromyces finnis, Neocallimastix californiae, Anaeromyces robustus, and Neocallimastix sp S4. Exemplary inoculant material includes particulate material which has been colonized by the fungal organism(s). As opposed to free zoospores, using such material as the starting inoculum leads to more vigorous growth and a substantial reduction in culture lag. The inoculated biomass is then allowed time to digest. The precise digestion time will vary depending on (1) the composition and lability of the feedstock; (2) the particulate size of the feedstock; (3) the concentration of inoculant; and (4) the specific bioreactor design. End-products of the digestion may be removed from the bioreactor at set intervals, continuously, or at the end of the digestion process. Removal of ethanol may be accomplished using methods known in the art for separation of ethanol from fermentation broth. Likewise, evacuation of hydrogen gas produced by the digestion may be accomplished utilizing means known in the art.

Working cultures of anaerobic fungi may require frequent sub-culturing in order to retain their viability. Most batch cultures remain viable for 5 or 15 days in media containing soluble (glucose) or particulate (reed canary grass) substrates, respectively. Frequent sub-culturing intervals of 2-7 days with growth on particulate substrates are generally employed to ensure the continued production of viable cultures.

The processes of the invention may optionally further encompass the co-culture of the described anaerobic gut fungi with other organisms to promote optimal production of bioenergy materials. For example, co-culture of anaerobic gut fungi with highly effective anaerobic fermenting organism, yeast or bacterial strains can result in an optimized system with efficient saccharization and fermentation. Similarly, production of specific end-products can be enabled by co-inoculation with organisms that convert the products of fungal digestion to other materials. For example, production of hydrogen through fungal hydrogenosome activity allows other microbes to reduce H₂ to the more energetically favorable methane gas. Co-culture with methane-producing organisms such as Archaea shifts end-product formation towards increased methane and acetate production, with a corresponding decrease in lactate, succinate, hydrogen and ethanol accumulation. In another embodiment, co-culture of anaerobic gut fungi with methanogens can be performed, which can significantly enhance the cellulose hydrolysis activity of the anaerobic fungi.

EXAMPLES Example 1. Sequence Identification

Fresh fecal material was collected from farm animals. Specimens were isolated from 5×10-fold serial dilutions of fecal matter in anaerobic buffer medium. Each dilution was then supplemented with 30 μg/ml chloramphenicol and grown in anaerobic medium containing milled reed canary grass at 39° C. to enrich for gut fungi. Enrichment cultures that were positive for fungal, but not bacterial or protist, growth after 5-10 days as determined by the generation of fermentation gases without an increase in culture turbidity were further subcultured. To generate unique fungal isolates, actively growing enrichment cultures were diluted up to 50-fold in serial dilutions with each dilution being subcultured for ˜4 days. This isolation procedure was repeated five times until a uniform fungal morphology was observed from each specimen and a unique ITS sequence of the isolate was obtained. Subsequent phylogenetic analysis of this ITS sequence confirmed the presence of a single novel fungal isolate in each culture. The new species were named Neocallimastix californiae, isolated from goat feces, Anaeromyces robustus, isolated from sheep feces, and Neocallimastix sp S4, isolated from sheep feces, and Piromyces sp. finn, isolated from horse feces.

To identify novel sequences of interest, each strain was grown in anaerobic medium supplemented with either glucose or milled reed canary grass at 39° C. After 2 days, the biomass was harvested and the total RNA extracted using the Qiagen RNeasy kit. This RNA was then enriched for mRNA by selecting for polyadenylated RNA and made into a strand specific cDNA library (single stranded). This cDNA library was then sequenced using an Illumina HiSeq next generation sequencing platform, using a standard workflow, and the resulting data was assembled into a de novo transcriptome using the TRINITY bioinformatics platform. The assembled sequences were then annotated with the BLAST2GO package by BLAST sequence alignment against known protein sequences and protein domain hidden Markov model (HMM) scans on Interpro of all possible translations of each transcript. The results were analyzed for statistical significance and sequences of interest were noted.

Example 2. Identification and Characterization of Scaffoldin Proteins

Genomic analysis of 5 unique anaerobic fungi revealed the presence of 1600 total dockerin domain proteins (DDPs) across genera with diverse functionality, primarily related to plant carbohydrate binding and biomass degradation. These include 15 glycoside hydrolase (GH) families, 5 distinct carbohydrate-binding domains, and other functions implicated in plant cell wall modification and deconstruction including pectin modifying enzymes and expansins. 20.2% of DDPs belong to spore coat protein CotH, which are also present in bacterial cellulosomes and are speculated to also be involved in plant cell wall binding. Conversely, 12.6% represent additional GH activities that are not present in bacterial cellulosomes (GH3, GH6, and GH45). The additional 3-glucosidase conferred by GH3 in particular enables fungal cellulosomes to convert cellulose directly to fermentable monosaccharides, whereas Clostridial cellulosomes produce low molecular weight oligosaccharides.

To find structural proteins that mediate assembly of DDPs, we isolated the supernatant and cellulosome fractions from three of these isolates growing on reed canary grass as a sole carbon substrate. Size-exclusion chromatography (SEC) of the cellulosome fraction showed complex formation well within the MDa range, and SDS-PAGE revealed the presence of many glycosylated proteins. Each fraction was subjected to tandem mass spectrometry and peptide sequences were mapped to their respective genomic and transcriptomic databases. Many of the proteins associated with these complexes were identified as GHs and other plant cell wall degrading enzymes. Proteins found in the cellulosome fraction were particularly enriched with NCDDs, indicating modular complex formation. Unexpectedly, all fractions also contained very large uncharacterized proteins (hereafter named ScaA) with molecular weights (MW) of approximately 700 kDa. These ScaA proteins share 32% sequence identity over at least 92% sequence length (E value=0.0) between fungal genera. ScaA orthologs were also detected in the only other sequenced gut fungal genomes, Piromyces sp. E2 and Orpinomyces sp. C1A, though the ortholog detected in O sp. C1A was incomplete likely due to fragmented genome assembly.

Sequence analysis of these proteins across all 5 sequenced genomes showed a predicted N-terminal signal sequence followed by a large extracellular repeat-rich domain, and ending with C-terminal membrane anchor. Some of these proteins also encode predicted choline binding repeats (CBRs), which are known to bind glucan in prokaryotic glucosyltransferases. Thus, one possibility is that CBRs help mediate fungal cellulosome assembly, as many cellulosome proteins are glycosylated. Closer examination of the sequences revealed the presence of a repeating amino acid sequence motif that is conserved among all of these homologues, and that occurs many times throughout these proteins. This motif is 20-30 amino acids long, typically includes with a Gly residue immediately followed by two large hydrophobic residues (most often Tyr residues) and two non-consecutive downstream Cys residues.

Because these proteins are highly represented in secretome and cellulosome fractions from these diverse species of gut fungi, we hypothesized that they share a common role in these systems, possibly in DDP assembly. We hypothesized that these proteins function as scaffolds whereby the repeating motifs act as dockerin-binding cohesins. To investigate this, we recombinantly expressed fragments of the ScaA homologues in Escherichia coli and performed enzyme linked immunosorbent assay (ELISA) using purified dockerin and anti-dockerin chemiluminescent secondary antibody. These results showed a strong dockerin binding signal in wells containing the scaffoldin fragment cells compared to those containing the empty vector control. As an additional control, a phenylalanine substitution to dockerin residue W28, previously identified to be critical for binding, showed significantly reduced binding activity. To determine the binding affinity of dockerin-ScaA interaction, we purified Piromyces ScaA fragments and performed equilibrium analysis by surface plasmon resonance (SPR) against purified fungal dockerin. This analysis revealed that a single dockerin domain interacts with the scaffoldin fragment with an approximate dissociation constant (K_(d)) of 0.7 μM and a maximum response (R_(max)) of 80 RU. Additionally, the W28F dockerin mutant showed significantly reduced binding affinity (K_(d), =2.0 μM, R_(max)=40 RU). Taken together, these results suggest that fungal scaffoldin proteins likely mediate assembly of DDPs in fungal cellulosomes.

Though limited, previous studies have shown that fungal cellulosomes are quite divergent from their bacterial counterparts. For example, NCDDs occur as tandem repeats at the N- and/or C-terminus, with the most common form being a double tandem repeat (i.e. double dockerin) at the C-terminus. Though the functional role of this motif repetition is not known, it has been previously noted that double dockerins bind to native cellulosomes more efficiently than single domains⁵. Thus, we hypothesized that increasing the number of NCDD from one to two could enhance binding affinity to the scaffoldin fragment. By ELISA, we found that the P. finnis single dockerin domain had higher binding affinity than the double dockerin domain. However, by SPR, the double dockerin had a comparable K_(d), but a higher R_(max) 120 RU, suggesting that the double dockerin is indeed capable of binding to more sites on the ScaA fragment than the single dockerin, which suggests that site specificity may be more subtly encoded in the different dockerin domains and cohesin repeats. Though the minimum sequence that defines a single cohesin remains to be determined, it is clear from our study that fragments of the scaffoldin encoding as few as four repeats are sufficient for dockerin assembly. Additionally, we cannot rule out that additional binding factors (e.g. glycosylation) found in native cellulosomes likely further modulate the fungal dockerin-cohesin interaction, which are lacking in this recombinant system.

It has previously been reported that dockerins are capable of binding to cellulosome fractions from other species of gut fungi, which is a marked departure from bacterial cellulosomes. In agreement with this observation, a Piromyces dockerin is capable of binding to intact cellulosome fractions harvested from Anaeromyces and Neocallimastix species. Thus, we tested whether this cross-species binding activity is encoded specifically within ScaA homologues. To test this, we purified single dockerin domains from all three genera of gut fungi and tested their ability to bind to all combinations of ScaA fragments. Indeed, we observed binding for all combinations tested and the binding signal was within standard error for almost all cases. Taken together, these results demonstrate that the fungal scaffoldin system is broadly conserved across the anaerobic fungal phylum, allowing for high interspecies infidelity. Therefore, it is not unreasonable to speculate that in their native environments, for example the dense microbial community of the herbivore rumen, fungal cellulosomes are a composite of enzymes from several species of gut fungi. This is in stark contrast to bacterial cellulosomes, which have high species specificity. This promiscuity may confer a selective advantage of fungi over bacteria in these environments.

In addition to the ScaA orthologs, other scaffoldin-like proteins were also detected through proteomic analysis of cellulosome-associated proteins. We tested three of these scaffoldins for dockerin binding activity and each tested positive over an empty vector control, suggesting that multiple scaffoldins likely exist in fungal cellulosomes. To search for scaffoldin-like proteins more broadly within anaerobic fungi, we developed a Hidden Markov Model (HMM) based on the repeating motif from all 6 scaffoldins biochemically verified to interact with dockerins. We found 95 unique loci in the genomes of A. robustus, P. finnis, and N. californiae, that bear a signal peptide and at least 10 cohesin repeats. Fewer loci (14) were detected in P. sp. E2 and 0. sp. C1A due to fragmented genome assemblies. Significantly, no loci were found in prokaryotes (2000 genomes) and only 1 or 2 weak hits in other fungi (˜400 genomes), demonstrating this HMM is highly specific to fungal scaffoldins. These results indicate that gut fungi likely produce multiple scaffoldins for cellulosome assembly, and these scaffoldins represent a new family of genes that is unique to the early branching anaerobic fungi.

While fungal scaffoldins and their NCDD ligands are specific to gut fungi, many plant biomass degrading enzymes that encode NCDDs are of bacterial origin, which has been noted previously for a limited subset of enzymes. Indeed, all five gut fungal genomes sequenced to date have large numbers of genes that are more similar to bacterial than to eukaryotic genes (9-13%). We aligned 1600 DDPs of the 5 anaerobic fungal genomes with the 394 fungi currently deposited in JGI MycoCosm (excluding Neocallimastigomycota) and the 1774 bacteria and archaea in JGI Integrated Microbial Genomes (IMG). Of these proteins, 611 aligned better with bacterial than fungal proteins and 158 aligned exclusively with bacteria. Conversely, only 38 aligned exclusively with fungi, and 372 aligned better to fungi than to bacteria. The remaining DDPs aligned equally with IMG and MycoCosm protein (3) or did not align with either (418). To determine whether this bacterial resemblance is the result of inter-kingdom horizontal gene transfer (HGT), we queried the domains that are fused to NCDDs to extract homologous sequences from the same bacterial and fungal genomes. When possible, we built phylogenetic trees of the domain sequences. Out of 35 non-dockerin domains analyzed, 10 (29%) passed our 2 criteria of 1) greater amino acid similarity to bacterial than to fungal sequences and 2) branching with bacterial rather than fungal sequences in its phylogenetic tree with >70% bootstrap support. The list of domains with an HGT signature includes 9 CAZyme domains as well as the spore coat domain. However, this analysis does not inform us as to the direction of any possible HGT events. Subjecting NCDDs to the same analysis showed that there are no similar sequences in IMG at all, suggesting that many DDPs may be fusions between native fungal and horizontally transferred bacterial components. Intriguingly, we found 12 fungal-bacterial homolog pairs where the bacterial protein is also a bacterial dockerin-domain protein. However, the sequence similarity between each pair of homologs encompasses only the catalytic domain and does not extend into the respective dockerin domains.

Over the past several decades, characterization of cellulosomes in fungi has been elusive, with multiple studies suggesting conflicting scaffolding schemes. Here, next-generation sequencing combined with functional proteomics uncovered a new family of genes that likely serve as scaffoldins in the cellulosomes of anaerobic fungi. The evidence for this is 3-fold: (1) scaffoldins appear among the most represented proteins in supernatant and cellulosome fractions in three diverse isolates of gut fungi, and their amino acids sequences encode hallmarks of a membrane-anchored scaffoldin molecule, including an N-terminal secretion motif, a C-terminal membrane anchor, and repeating amino acid motif in between. These scaffoldins are encoded in all sequenced Neocallimastigomycota (representing 4 of the 8 genera of gut fungi identified to date) and absent in other fungi. (2) Expression of repeat-containing scaffoldin fragments shows robust interaction with purified dockerins by ELISA. (3) This dockerin-scaffoldin interaction is biologically significant (K_(d)≈0.7 uM) as measured by SPR, whereas a mutated dockerin derivative significantly reduced binding activity. Taken together, the identification of a new dockerin-binding protein scaffold from fungi opens the way for exploitation of this modular interaction for synthetic biology and substrate channeling. Finally, the powerful degradation activity of gut fungi is provided by the diverse functionality of its constituents, with 50 unique protein families of bacterial and fungal origin, and the assembly of these constituents onto scaffoldin molecules into cellulosome-like complexes. Perhaps the most intriguing observation from this study is that fungal dockerins and their scaffoldin ligands have no sequence similarity to their bacterial counterparts. Thus, it is possible that the cellulosome-based strategy for plant cell wall degradation evolved in anaerobic gut fungi independently of bacteria. This suggests that co-localizing plant cell wall degrading enzymes is so effective that nature has evolved it on more than one occasion.

Example 3. Characterizing the Production of Secondary Metabolites in Anaerobic Fungi

In order to better understand the production of secondary metabolites by the anaerobic fungi of the invention, bioinformatics tools and analytical tools were employed. It was determined that numerous genes involved in the production of secondary metabolites were actively transcribed in Piromyces finnis, Anaeromyces robustus, and Neocallimastix californiae. Genes involved in secondary metabolite production included PKS genes as well as genes involved in the synthesis of nonribosomal peptides, terpenes, fatty acids, bacteriocins, and others.

Additionally, LC-MS/MS analysis of fungal products was performed, and a large number of peaks were observed, each corresponding to a composition having unique mass and charge. These results provide promising experimental evidence that secondary metabolites are produced in abundance by these anaerobic fungi.

All patents, patent applications, and publications cited in this specification are herein incorporated by reference to the same extent as if each independent patent application, or publication was specifically and individually indicated to be incorporated by reference. The disclosed embodiments are presented for purposes of illustration and not limitation. While the invention has been described with reference to the described embodiments thereof, it will be appreciated by those of skill in the art that modifications can be made to the structure and elements of the invention without departing from the spirit and scope of the invention as a whole. 

What is claimed is:
 1. A hydrogen-producing organism, wherein the hydrogen-producing organism is engineered to express one or more glycoside hydrolase proteins, wherein the one or more glycoside hydrolase proteins comprises at least 80% sequence identity to a polypeptide sequence selected from the group consisting of: SEQ ID NO: 1298-1303; SEQ ID NO: 9757-10818; SEQ ID NO: 10824-10913; SEQ ID NO: 10871-10986; SEQ ID NO: 10990-11313; SEQ ID NO: 11511-1560; and SEQ ID NO: 11670-11844.
 2. The hydrogen producing organism according to claim 1, wherein the hydrogen producing organism is selected from the group consisting of Saccharomyces cerevisiae, Zymomonas mobilis, Escherichia coli, Clostridium thermocellum, and a fungal species.
 3. The hydrogen-producing organism according to claim 1, wherein the hydrogen producing organism further comprises one or more catalytic enzymes capable of digesting lignocellulosic biomass selected from the group consisting of: cellobiohydrolase, Beta-D-glucan exohydrolase, dehydrogenases, glycoside hydrolase, and ketoreductase.
 4. The hydrogen producing organism according to claim 1, wherein the hydrogen producing organism is combined in a co-culture with a lignocellulosic biomass-digesting organism comprising at least one or more catalytic enzymes capable of digesting lignocellulosic.
 5. The hydrogen-producing organism according to claim 1, wherein the hydrogen-producing organism further expresses one or more glycosyl hydrolase proteins, wherein the one or more glycosyl hydrolase proteins comprises a sequence having at least 80% identity to a sequence selected from the group consisting of SEQ ID NO: 3963-3972; SEQ ID NO: 9749-9756; SEQ ID NO: 10866-10870; SEQ ID NO: 10987-10989; SEQ ID NO: 11314-11361; SEQ ID NO: 11362-11510; and SEQ ID NO: 11561-11648.
 6. The hydrogen-producing organism according to claim 1, wherein the one or more glycoside hydrolase proteins is expressed in an engineered protein; wherein the engineered protein comprises a dockerin domain; and wherein the engineered protein is produced and is subsequently extracted from the hydrogen-producing organism.
 7. The hydrogen-producing organism according to claim 1, wherein the hydrogen-producing organism further expresses one or more dehydrogenase proteins, wherein the one or more dehydrogenase proteins comprises a sequence having at least 80% identity to a sequence selected from the group consisting of: SEQ ID NO. 800-862; SEQ ID NO: 6319-6322; SEQ ID NO: 9728-9748; SEQ ID NO: 11925-11933; and SEQ ID NO: 13196-13207.
 8. The hydrogen-producing organism according to claim 6, wherein the dockerin domain is fused with a carbohydrate-binding element from an organism selected from a bacterial species, a yeast species, a fungal species, or a plant species.
 9. The hydrogen-producing organism according to claim 4, wherein the co-culture is further comprises a yeast strain or bacterial strain, or a combination of a yeast strain with a bacterial strain.
 10. The hydrogen-producing organism according to claim 1, wherein the hydrogen-producing organism is a species selected from the group consisting of a bacterial species, a yeast species, a fungal species, or a plant species.
 11. The hydrogen-producing organism according to claim 10, wherein the one or more glycoside hydrolase proteins is produced by and is subsequently extracted from the hydrogen-producing organism.
 12. The hydrogen producing organism according to claim 11, wherein the one or more glycoside hydrolase proteins is expressed in an engineered multiple enzyme complex, and is produced by and subsequently extracted from the hydrogen-producing organism.
 13. The hydrogen-producing organism according to claim 1, wherein the hydrogen-producing organism is a cultured anaerobic fungal species selected from the group consisting of Piromyces finnis, Neocallimastix californiae, Anaeromyces robustus, and a Neocallimastix sp S4.
 14. A hydrogen-producing organism, wherein the hydrogen-producing organism is engineered to express one or more glycosyl hydrolase proteins, wherein the one or more glycoside hydrolase proteins comprises a polypeptide sequence having at least 80% sequence identity to a polypeptide sequence selected from the group consisting of: SEQ ID NO: 3963-3972; SEQ ID NO: 9749-9756; SEQ ID NO: 10866-10870; SEQ ID NO: 10987-10989; SEQ ID NO: 11314-11361; SEQ ID NO: 11362-11510; and SEQ ID NO: 11561-11648.
 15. The hydrogen-producing organism according to claim 14, wherein the hydrogen-producing organism further comprises one or more catalytic enzymes capable of digesting lignocellulosic biomass.
 16. The hydrogen-producing organism according to claim 14, wherein the hydrogen-producing organism is combined in a co-culture with a lignocellulosic biomass-digesting organism comprising one or more catalytic enzymes capable of digesting lignocellulosic biomass.
 17. The hydrogen producing organism according to claim 14, wherein the hydrogen-producing organism further comprises one or more catalytic enzymes capable of digesting lignocellulosic biomass.
 18. A hydrogen-producing organism, wherein the organism is engineered to expresses one or more dehydrogenases, wherein the one or more dehydrogenases comprises a polypeptide sequence having at least 80% identity to a sequence selected from the group consisting of: SEQ ID NO. 800-862; SEQ ID NO: 6319-6322; SEQ ID NO: 9728-9748; SEQ ID NO: 11925-11933; and SEQ ID NO: 13196-13207.
 19. The hydrogen-producing organism according to claim 18, wherein the one or more dehydrogenases is produced by and is subsequently extracted from the hydrogen-producing organism.
 20. The hydrogen producing organism according to claim 18, wherein the hydrogen producing organism is combined in a co-culture with a lignocellulosic biomass-digesting organism comprising at least one or more catalytic enzymes capable of digesting lignocellulosic biomass. 